Sat Oct 8 11:35:28 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 11:35:28 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4209 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5508789 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -3.452000 61.17200 ymin,ymax (A): -12.89400 38.37500 zmin,zma (A): -18.55500 45.07300 x,y,z range (A): 64.62400 51.26900 63.62800 scale (grids/A): 0.5508789 object centre (A): 28.86000 12.74050 13.25900 number of atom coordinates read : 4209 total number of charged atoms : 4056 net assigned charge : -2.485934 assigned positive charge : 633.7749 centred at (gu) : 89.12440 89.94926 90.57104 assigned negative charge : -636.2635 centred at (gu) : 89.19172 90.04166 90.64184 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8168 nv = 96 ne = 84 npr = 88802 no. pairs analyzed = 88802 no. exposed pairs = 4850 no. arc points = 32305 no. surface atoms = 1659 nbur = 2550 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 314 mr = 4621 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3358 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2893290E-10 -1.1565010E-09 midg,1,midg; midg,igrid,midg 8.6318325E-10 -1.2390347E-09 1,midg,midg; igrid,midg,midg 7.1489847E-10 -7.7615214E-10 gauss-seidel spectral radius is 0.9830918 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 11:35:29 rms-change max change #iterations 9.2076801E-02 12.59058 at 10iterations 6.7414842E-03 0.9504890 at 20iterations 9.4109640E-04 0.1273575 at 30iterations 2.8814829E-04 4.2461395E-02 at 40iterations 9.9254190E-05 1.5094757E-02 at 50iterations finished qdiffx linear iterations at : 11:35:32 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 9.9254190E-05 1.5094757E-02 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 11:35:33 3.876u 0.251s 0:04.40 93.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 11:35:33 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4209 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.652637 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -3.452000 61.17200 ymin,ymax (A): -12.89400 38.37500 zmin,zma (A): -18.55500 45.07300 x,y,z range (A): 64.62400 51.26900 63.62800 scale (grids/A): 1.652637 object centre (A): 28.86000 12.74050 13.25900 number of atom coordinates read : 4209 total number of charged atoms : 4056 net assigned charge : -2.485934 assigned positive charge : 633.7749 centred at (gu) : 87.37187 89.84663 91.71200 assigned negative charge : -636.2635 centred at (gu) : 87.57454 90.12443 91.92503 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32305 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29590 mr = 66176 m= 3197 mr = 21194 m= 104 mr = 1668 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1548 time to turn everything in is 0.4600000 number of dielectric boundary points 35470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 31118 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5508789 object centre at (A) : 28.86000 12.74050 13.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1411563E-04 -1.3847234E-02 midg,1,midg; midg,igrid,midg 4.2047086E-03 -1.9476442E-02 1,midg,midg; igrid,midg,midg 1.9250821E-02 2.0807464E-02 gauss-seidel spectral radius is 0.9983432 estimated iterations to convergence 195 setup time was (sec) 0.7100000 now iterating at: 11:35:34 rms-change max change #iterations 4.156228 194.1206 at 10iterations 1.798225 59.75198 at 20iterations 0.7822523 26.03034 at 30iterations 0.3394472 10.63395 at 40iterations 0.1476588 4.310341 at 50iterations 6.4214274E-02 2.028633 at 60iterations 2.8057083E-02 1.018795 at 70iterations 1.2339929E-02 0.3648491 at 80iterations 5.4587713E-03 0.1641388 at 90iterations 2.4888776E-03 8.1230164E-02 at 100iterations 1.1839985E-03 3.6436081E-02 at 110iterations 6.0983031E-04 2.0184517E-02 at 120iterations finished qdiffx linear iterations at : 11:35:42 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 6.0983031E-04 2.0184517E-02 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.820000 DelPhi exited at 11:35:42 8.824u 0.249s 0:09.34 97.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 11:35:42 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4209 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.478955 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -3.452000 61.17200 ymin,ymax (A): -12.89400 38.37500 zmin,zma (A): -18.55500 45.07300 x,y,z range (A): 64.62400 51.26900 63.62800 scale (grids/A): 2.478955 object centre (A): 28.86000 12.74050 13.25900 number of atom coordinates read : 4209 total number of charged atoms : 4056 net assigned charge : -2.485934 assigned positive charge : 633.7749 centred at (gu) : 86.05734 89.76973 92.56773 assigned negative charge : -636.2635 centred at (gu) : 86.36180 90.18658 92.88739 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 213367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32305 grid for indexing accessible points = 1.400000 m= 103015 mr = 161445 m= 29836 mr = 83716 m= 5141 mr = 22950 m= 395 mr = 3548 m= 12 mr = 159 m= 0 mr = 3 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 5307 time to turn everything in is 1.160000 number of dielectric boundary points 79945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 32414 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.652637 object centre at (A) : 28.86000 12.74050 13.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2835115 -0.2764435 midg,1,midg; midg,igrid,midg 4.8157107E-02 -0.2626046 1,midg,midg; igrid,midg,midg 0.4368835 0.2882054 gauss-seidel spectral radius is 0.9992102 estimated iterations to convergence 281 setup time was (sec) 1.460000 now iterating at: 11:35:44 rms-change max change #iterations 10.69008 250.9058 at 10iterations 6.175143 126.6694 at 20iterations 3.542059 72.65907 at 30iterations 2.027968 42.01360 at 40iterations 1.157493 22.86732 at 50iterations 0.6591758 12.21271 at 60iterations 0.3741500 6.864418 at 70iterations 0.2121864 3.603287 at 80iterations 0.1201701 2.665298 at 90iterations 6.8136074E-02 1.249308 at 100iterations 3.8579650E-02 0.7285690 at 110iterations 2.1873819E-02 0.4032993 at 120iterations 1.2402351E-02 0.2289295 at 130iterations 7.0605357E-03 0.1191101 at 140iterations 4.0475032E-03 7.5069427E-02 at 150iterations 2.3443266E-03 4.2072296E-02 at 160iterations 1.3812321E-03 2.6935577E-02 at 170iterations 8.4274961E-04 1.4967680E-02 at 180iterations finished qdiffx linear iterations at : 11:35:58 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 8.4274961E-04 1.4967680E-02 energy calculations done at 15.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 11:35:59 15.865u 0.291s 0:16.43 98.2% 0+0k 0+0io 0pf+0w